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Sodium in PDB 5kqn: Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei

Enzymatic activity of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei

All present enzymatic activity of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei:
1.11.1.21;

Protein crystallography data

The structure of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kqn was solved by P.C.Loewen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.18 / 1.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 100.986, 114.174, 175.544, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.2

Other elements in 5kqn:

The structure of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei (pdb code 5kqn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei, PDB code: 5kqn:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5kqn

Go back to Sodium Binding Sites List in 5kqn
Sodium binding site 1 out of 2 in the Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na802

b:20.6
occ:1.00
O A:GLY122 2.3 19.4 1.0
O A:GLY124 2.3 20.2 1.0
O A:HOH960 2.3 25.9 1.0
O A:SER494 2.3 22.3 1.0
O A:HOH995 2.5 22.9 1.0
C A:SER494 3.2 21.6 1.0
C A:GLY124 3.5 18.4 1.0
C A:GLY122 3.5 19.1 1.0
CA A:ARG123 3.5 18.3 1.0
C A:ARG123 3.5 17.9 1.0
N A:GLY124 3.6 19.3 1.0
O A:HOH1421 4.0 25.3 1.0
CA A:SER494 4.0 20.6 1.0
N A:ARG123 4.0 19.3 1.0
OD2 A:ASP427 4.0 23.5 1.0
N A:ASP495 4.1 18.0 1.0
O A:ARG123 4.1 19.8 1.0
CA A:GLY124 4.1 18.9 1.0
O A:HOH1023 4.1 30.4 1.0
CB A:ASP427 4.2 24.0 1.0
CB A:SER494 4.2 22.2 1.0
CA A:ASP495 4.4 19.6 1.0
N A:GLY125 4.6 17.3 1.0
CB A:ASP495 4.6 21.4 1.0
CD1 A:TYR117 4.6 20.7 1.0
CG A:ASP427 4.7 22.2 1.0
OE1 A:GLU198 4.7 28.2 1.0
CA A:GLY122 4.7 20.7 1.0
OE2 A:GLU198 4.7 40.8 1.0
CE1 A:TYR117 4.8 22.0 1.0
CA A:GLY125 4.8 17.2 1.0
CB A:ARG123 4.8 21.5 1.0
OE2 A:GLU128 4.9 40.1 1.0

Sodium binding site 2 out of 2 in 5kqn

Go back to Sodium Binding Sites List in 5kqn
Sodium binding site 2 out of 2 in the Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the H381S Variant of Catalase-Peroxidase From B. Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na802

b:21.5
occ:1.00
O B:HOH994 2.2 24.5 1.0
O B:SER494 2.4 23.1 1.0
O B:GLY124 2.4 20.9 1.0
O B:HOH963 2.4 25.3 1.0
O B:GLY122 2.4 20.2 1.0
C B:SER494 3.2 23.3 1.0
C B:GLY124 3.5 21.2 1.0
C B:GLY122 3.5 18.5 1.0
C B:ARG123 3.6 19.5 1.0
N B:GLY124 3.6 19.4 1.0
CA B:ARG123 3.6 18.8 1.0
CA B:SER494 4.0 21.4 1.0
O B:HOH1341 4.0 22.1 1.0
O B:HOH990 4.0 37.4 1.0
N B:ARG123 4.1 19.4 1.0
OD2 B:ASP427 4.1 24.9 1.0
N B:ASP495 4.1 18.8 1.0
CB B:ASP427 4.1 22.2 1.0
CA B:GLY124 4.2 21.8 1.0
CB B:SER494 4.2 20.4 1.0
O B:ARG123 4.2 19.2 1.0
CA B:ASP495 4.4 21.1 1.0
CB B:ASP495 4.5 21.4 1.0
N B:GLY125 4.6 19.0 1.0
CD1 B:TYR117 4.6 21.7 1.0
OE2 B:GLU198 4.7 41.7 1.0
CG B:ASP427 4.7 23.6 1.0
OE1 B:GLU198 4.8 27.4 1.0
CA B:GLY122 4.8 20.5 1.0
CE1 B:TYR117 4.8 20.9 1.0
OE2 B:GLU128 4.9 41.9 1.0
CA B:GLY125 4.9 20.6 1.0
CB B:ARG123 4.9 21.7 1.0
OG B:SER494 5.0 21.9 1.0
O B:HOH1181 5.0 35.1 1.0

Reference:

P.C.Loewen, P.C.Loewen. N/A N/A.
Page generated: Tue Dec 15 11:10:59 2020

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